


The End of Hope's Peak Academy

by orphan_account



Category: Dangan Ronpa - All Media Types, Dangan Ronpa 3: The End of 希望ヶ峰学園 | The End of Kibougamine Gakuen | End of Hope's Peak High School
Genre: Alternate Ending, Bittersweet Ending, Declarations Of Love, F/M, Gen, updated with an alternate alternate ending
Language: English
Status: Completed
Published: 2016-08-07
Updated: 2017-04-14
Packaged: 2018-07-29 14:57:40
Rating: Teen And Up Audiences
Warnings: Major Character Death
Chapters: 2
Words: 4,298
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/7688959
Author URL: https://archiveofourown.org/users/orphan_account/pseuds/orphan_account
Summary: <blockquote class="userstuff">
              <p>This is the way the story ends. </p><p>Written before Ep.5 of DR3 Future Arc was shown, so I tried to keep it canon up to there. There is one other ship, but it would spoil the story to add it in to the tags.</p><p>update: this fic now has an alternate ending where it doesn't pull the wool over your eyes about the ship.</p>
            </blockquote>





	1. The original fic

The Final Killing Game, despite not initially having gone to plan, was achieving its goal. The Future Foundation had been wiped out almost entirely, with only five of its key members remaining. Though only five had been lost in the game itself - six, if counting the false Miaya Gekkougahara - several had fallen to Monaca Towa and her brainwashed, Monokuma-masked army of foot soldiers, which had been taken to the streets of Tokyo. The population, already ravaged by the Tragedy, had once again been decimated by the war between the Future Foundation and the remainder of Ultimate Despair.

On a red-skied evening, in the midst of one battle, Makoto Naegi and Kyouko Kirigiri found themselves in a hollow shell of a building. They, being the members of the Foundation who were least capable in direct combat, were sent there to take cover while the others went to take on Monaca and her troops head-on. Still, they were under orders from Kyousuke Munakata, their leader and general, and at any moment he could contact either one of them to join the fight. Explosions and the sound of bodies falling rang out from outside the doorway, with both Makoto and Kyouko seated behind the wall just beside the doorway, concealing themselves from - and ready to attack - anyone who tried to enter. 

As Makoto tried his hardest to tune out the carnage behind him, his mind turned to Kyouko, who even in a situation like this retained an ice-like cool as she analysed every crack she could see around her, watching for any sudden movement. Anyone would have to admit that he and Kyouko had come a long way; he couldn't say much for the memories they had lost, but they had become true allies and friends in the Killing Game, where they were able to inspire each other and bring victory over Junko Enoshima. She had become important to him during the endless conflict and danger, and he couldn't think what would happen if he were to see her killed in this last struggle against despair.

He remembered what he could of class 78, the other four survivors of the Killing Game having been killed since his hearing. Yasuhiro Hagakure was the first to go; after Monaca had revealed herself and ordered her forces to launch an all-out attack on the Future Foundation headquarters, he had been trapped outside, never receiving the orders of Munakata to attempt an escape, and he was quickly overcome by missile fire. Byakuya Togami was next to die, captured and beaten to death in the city by a pair of Monokuma-masked men. When Touko Fukawa discovered his body, she was incapable of overcoming the despair of losing her love, and she was found the next day curled around him and dead of shock. The latest to fall was one whom Makoto had already thought to be dead: Aoi Asahina, who had taken to the front lines inspired by the two she was closest to, Sakura Oogami and her brother Yuta. She fought hard and well, but was eventually overpowered and killed.

Makoto didn't even want to consider the prospect of losing Kyouko, one of the last people in the world he could hold dear to him, and being unable to save her. But he knew in his heart that it was inevitable; the Future Foundation forces would need the extra power to finish the fight. And sure enough, Kyouko raised her communicator to her ear, receiving contact. "Yes, Munakata. Understood." After scanning behind her once more, she rose from the seated position, still with her back to the wall that hid both her and Makoto from any invading threat, and quietly spoke three words to her partner in arms: "I'm going in."

Almost instinctively, Makoto moved to grab Kyouko's arm. "Don't! You'll get killed out there! And after everyone we've lost in this fight, we..." He hesitated for a moment. "I can't afford to lose you, too."

Makoto's words stirred something in Kyouko, and he could swear that her usual steely calm had softened a touch. She needed a few seconds before she could respond.

"No, I must. They need the numbers to overcome Monaca once and for all, and I have decided to go. But I have one thing that I need to say, in case we never see each other again: I love you. I love you, Makoto Naegi, and I always have, and I always will."

Makoto moved to reply: "And I--" The words froze in his throat. He swore he could feel another fragment of his lost memories returning, and he clutched his head in pain. This regularly happened to the Class 78 survivors, though most often to Makoto (as a certain Ultimate Therapist would have said, it was perhaps because memories were most precious to him). Usually it was something light, like the time he helped a fellow student out or a memorable class trip, but this time it was serious. Serious enough that it had stopped his intended response to Kyouko's confession in its tracks. In fact, any response at all was a no-go as he continued to deal with the rush of old memories back to his mind.

Kyouko said nothing and left to join the battle, not letting her face betray even an ounce of dismay.

\--

It wasn't until the next morning that Makoto received the news, both good and horrifying: Monaca had been slain in his absence, but Kyouko had perished in the fight too. It would be fairly simple work, he was told, to eliminate the last pockets of Ultimate Despair-aligned groups in Japan. But Kyouko Kirigiri, his last true ally in both the fight against despair and the fight to clear his name, was dead. Gone forever. And Makoto began to feel the first twinges of despair that he had felt in years. In the calm morning after the enemy had lost their leader, he was able only to curl up, head down, in the same abandoned building where he had last seen Kyouko, and think about nothing at all.

It took Makoto four hours to look up from his state of numbness. There, he saw Kyousuke Munakata, who, unbeknownst to Makoto, had entered and was now looking down on him.

Kyousuke spoke when the other looked up, his face hard and disapproving as always. "Naegi... It seems what you said is true. Ultimate Despair will soon be overcome after all. Honestly, I never doubted your abilities to ensure that hope would always remain victorious. Now, it seems I must confess a truth about myself."

Makoto sat and listened to Kyousuke attentively (well, attentively as he could, being that he was still grieving for Kyouko).

Kyousuke began: "I was a classmate of theirs. Juzo Sakakura... and Chisa Yukizome. I entered Hope's Peak Academy four years before you, with the same naïve idealism that you seemingly still have. They called me the 'Ultimate Student Council President', because I had the drive to lead and to enforce order, and I can't say they were wrong in their judgement. I happened to graduate just before the class that would become Ultimate Despair entered, and I was soon employed to aid in developing an overseas branch of Hope's Peak.

"That, naturally, earned me several meetings with Headmaster Kirigiri, and a glimpse into the inner workings of the Academy. The Headmaster... he was ultimately well-meaning, but weak. You'd think he held all the power over the way the Academy turned, but he was ultimately a puppet for the Steering Committee: a group of dreadful old men who cared little for the welfare of the students if it would prevent them from achieving their twisted goals. When I overheard talk of the culmination of the research of talent that had driven Hope's Peak for so many years, I sent Yukizome, who had recently begun to teach at the school, to aid my investigation of their intentions. What we found was truly horrifying: they planned to create superhumans out of ordinary Reserve Course students, destroying their identity and making them nothing but tools for the committee's potential whims.

"Naturally, I couldn't bring up the issue with the Headmaster, as he was powerless to stop it, and it would only label me as a defector, putting me at the mercy of the Steering Committee. So I had only one possible course of action: destroying the whole operation from the inside. I just had to find one student who could further my goal. It happened that a new class of students had recently entered the academy, and out of them, one stood out. Junko Enoshima. The Ultimate Fashionista, she could easily influence her fellow students, and on top of that I saw raw destructive energy inside her, which would be more than enough to bring about the chaos that would bring Hope's Peak Academy down. So I enabled her: I tried to shoot down all the issues surrounding her education, and I convinced Headmaster Kirigiri to fight her corner before the Steering Committee whenever she was judged to be a serious threat.

"It worked... far too well. Enoshima managed to convince her vulnerable upperclassmen to join her cause. She was somehow able to place an entire area of the building under lockdown, forcing the Student Council, including the successor to my title - as well as the Steering Committee's first test subject, Izuru Kamukura - into a mutual killing scenario. Soon, Kamukura was the only one left alive, and seeing that their money and hard work had only funded murders pushed the rest of the Reserve Course over the edge, sparking a revolution which led to the Tragedy: the most dreadful, despair-inducing incident in the history of mankind.

"I told you before, Makoto Naegi," concluded Kyousuke, "that you could never be a true hope, because you never knew true despair. True despair is watching your plan to save the students of Hope's Peak destroy them all, and the entire world with them."

Makoto could only gather the strength to reply: "But if you wanted to save the students of Hope's Peak Academy... why are you so intent on killing the rest of them now?"

Kyousuke's eyes, formerly locked into an intense stare in Makoto's direction, widened slightly.

"You have somewhat impressed me, Naegi," he said. "It's little wonder you managed to talk down Enoshima at the height of her power."

"In truth, my intent on killing the Remnants of Despair was little but a lie. I made my escape from the vicinity of Hope's Peak after the Reverse Course riots began, along with Yukizome and Sakakura. We had to go into hiding, but we survived long enough to find and rally together several former students and staff who were also still alive. Together we formed the Future Foundation. I, in charge of much of the major administration, presented the Foundation as an organisation with the altruistic goal of bringing down Ultimate Despair and restoring hope to the world. But my greater goal, in fact, was to pay penance to the world. I, however indirectly, had helped to engineer the event that brought humanity to its knees, so the least I could do was help it to rise up again.

"I never wanted to see the 77th class - the Remnants - dead. In fact, I wanted them to be safe from the evils of Hope's Peak all along, even after I inadvertently created a greater evil in its place. The only reason I ever claimed to want them all executed instead of rehabilitated is because the surviving population saw Ultimate Despair as a universal enemy, and the Future Foundation helping those who worked for the enemy instead of destroying them? That would make us wrong in their eyes. And in a time when we needed to be seen as the hope of the world for the people to rally behind, that could only be detrimental. So I put up this front of seeking the death of every one of them. In truth, I knew of them as ordinary students before the Tragedy, and they were wide-eyed and hopeful, like you are, and I once was. They were influenced by Enoshima in their darkest hour, and used as tools of despair; in short, they were human beings too, and deserved to be spared with the rest of the innocents.

"You, on the other hand, are someone about whom I have always been truthful.

"Your greatest asset to the Foundation is also your greatest weakness: your optimism, and your ability to inspire people. They were able to help the world see the Foundation as a force for good, and for hope. However, you could be influenced easily by anything, and in return go on to convince millions of people that what you say is true... which could be a great asset to any hidden Ultimate Despair who chooses to rise up. Now that the survivors of the Tragedy are behind the Future Foundation, the benefits of keeping you alive are far outweighed by the risks. Sakakura was one who saw that, and what did you and your friends do to him? You tied him up and killed him, just because he tried to show you the truth."

He seemed to reach for his katana, but changed his mind. He instead moved to his back pocket area, and revealed a gun, which he pointed squarely at Makoto's head. 

"I did what I had to do all my life, and now I'll do it again. Goodbye, Naegi."

Makoto did not have the energy to retaliate.

A shot rang out for a mile away, and the rest was silence.

\--

Kyousuke Munakata returned to meet the last of the Future Foundation-allied forces, who had fought so hard to take down Monaca, and address them. Before him stood a former Hope's Peak scout who had discovered the students who had brought down most of civilisation; a former Ultimate Pharmacist who had faced the deaths of those who she thought had betrayed her; and a girl who had overcome capture, learned to protect herself, and become an instrumental figure in the fight for hope, defeating Monaca twice.

He called them each by name. "Kizakura. Kimura." He paused for a moment. "Naegi." She would have to learn of her brother's death later; he would claim that he had been attacked by a lone Monokuma mask, just to soften the blow. "We must go to Jabberwock Island, to check on the status of the Remnants of Despair. They should have mostly recovered by now."

Leading them in a direction only he knew, he began a journey to the future, for the sake of hope.

\--

\--

\--

Makoto Naegi awoke in the halls of Hope's Peak Academy. Typical. He had been knocked out more than anyone needs to be in their life, so regaining consciousness in a strange location was almost an everyday occurrence to him.

Getting up to collect himself, he instictively brushed any dust away from the front of his hoodie, but was quickly met by Sayaka Maizono, who approached him as soon as she spotted him. Sayaka pulled him into a friendly hug, so happy to see her former classmate from junior high school again. She whispered a few words into his ear, then ran away again, motioning Makoto in her direction. Makoto, still a little stunned, chose to move forward.

Passing a few doors to classrooms which were seemingly uninhabited, he spotted the Ultimate Baseball Star, Leon Kuwata, leaning with his back to the wall. From his position, Leon looked at Makoto and winked, giving him two thumbs up. A few doors later, he passed Chihiro Fujisaki, wearing that inimitable smile of his which seemed to brighten up the area around him. Turning a corner, he spotted Kiyotaka Ishimaru and Mondo Oowada arm in arm, the two bringers of order and disorder laughing heartily, linked like brothers. The next stretch of hallway saw him find Hifumi Yamada, who looked up from whatever 2D fantasy he was in to look at Makoto in understanding, as well as Celestia Ludenberg, who stared at him for a while before giving a rare, genuine smile. The next corner brought Makoto to the colossal frame of Sakura Oogami, who looked into his eyes as if proud of him for something he did not understand.

Following the hallway, in which the turns only seemed to become more frequent, he met Yasuhiro Hagakure, who stepped up to shake his hand and let out a slight chuckle afterwards. He was soon followed by Byakuya Togami, whose constant look of superiority was betrayed by a sense of thankfulness for everything Makoto had done. Of course, Touko Fukawa was alongside him, almost clinging to him, and she seemed to concur with the thoughts of her "Master" as always. After another couple of turns, Makoto was met by Kyouko Kirigiri. She approached him, saying nothing, but took both of her hands in his and smiled. She eventually had to break the contact, still looking at Makoto as he passed. He made three more turns coming face to face with Junko Enoshima. It soon became apparent to Makoto that this was a very different Junko from his memory of her; she seemed to have a much more genuine posture and a look of friendliness - perhaps even hope - in her eyes.

Finally, Makoto reached the entrance to the gym hall, with Sayaka standing by the double doors. She held one side open, motioning him in. Giving one last look to Sayaka, Makoto took one step inside.

The students and staff of Hope's Peak Academy all surrounded the gym hall, looking at him in true pride. He saw walls of faces he would never have expected to see again. And in the centre of the gym, Makoto was able to see - for the first time that he could still remember - the real Mukuro Ikusaba. She looked at him, as if surprised to see him. He smiled at her, and she returned it, just like the first smile they had shared together: the one that had eventually made her fall for him. Delving deep into each other's eyes, Makoto finally realised what that rush of memories had been, and he moved up to Mukuro and held her in a tight embrace, kissing her repeatedly on the lips. At that point, all around him began to applaud, watching the two forgotten lovers reunited once more. Even Kyouko had joined them, with a few tears falling from her eyes in a rare event.

Makoto and Mukuro continued their embrace, not caring for anything around them, because they knew here, there would be no despair, no misfortune to get in their way. Hope was theirs once more.

**Notes for the Chapter:**

> Whoa. This was quite an undertaking.
> 
> I saw this theory once that Munakata finished his investigation of HPA, he realised how rotten an operation it all was, and began to destroy it from within by enabling one of the new students (that being a certain Junko Enoshima) to spread despair. That of course led me to think: what would a big reveal speech by Munakata to Naegi about what he had really planned be like? I then thought what would follow that, and I settled on the death of Naegi at Munakata's hand. I tried my hardest to make Munakata seem well-intentioned at heart, and if I didn't manage to do that, I'm truly sorry.
> 
> And of course you have the whole Titanic-ending style thing going on at the end. This entire work was conceptualised during a long shower I had, and I'm not ashamed to say that I legitimately tore up as I narrated an early version of it to myself. If it seems tacked on, then it probably was because I thought it was so damn good. I threw a curveball with the shameless ship at the end, just to subvert your expectations that this was going to end in a teary Naegiri reunion. Just call me Kodaka, the way I play with what you're thinking.
> 
> I hope you liked this story.


	2. Alternate ending (and pre-ending) - the Naegiri you were hoping for

**Summary for the Chapter:**

> so apparently some people didn't like the way the ship i was going for completely changed. this is an alternate ending where the naegiri i was leading up to actually happens, and i don't pull a shitty kodaka twist on you.
> 
> remember, this is an au! the original was written entirely before future arc episode 5.

Makoto's words stirred something in Kyouko, and he could swear that her usual steely calm had softened a touch. She needed a few seconds before she could respond.

"No, I must. They need the numbers to overcome Monaca once and for all, and I have decided to go. But I have one thing that I need to say, in case we never see each other again: I love you. I love you, Makoto Naegi, and I always have, and I always will."

Makoto was stunned. Was this the right time for a love confession, when either of them could be killed at any moment? Was it even a good idea to bring that out in the open before the conflict was over...? He stopped the line of thoughts in his head. Of course it was. This was Kyouko Kirigiri, and she always knew the right moment to come out and say something. In truth, what Makoto wanted to say was what Kyouko had just said, but the nerves and the fear made the words freeze in his throat. So instead, he decided to let his actions speak for his words, and brought his lips to hers. 

As soon as the kiss began, memories flooded like a bolt of lightning through Makoto's brain. This had regularly happened to the Class 78 survivors, though most often to Makoto (as a certain Ultimate Therapist would have said, it was perhaps because memories were most precious to him). Usually it was something light, like the time he helped a fellow student out or a memorable class trip, but sometimes it could be a darker memory - for example, most of his memories of Junko Enoshima - that he would much rather keep forgotten. This time, the memories were only warmth. Of a girl with lavender hair and cold demeanor approaching him to ask for his accompaniment on an investigation. Of all the times their hands had accidentally brushed each other, resulting in blushes and apologies that he had no reason to give. Of their first kiss - their _real_ first kiss, in happier times that Despair had tried to snatch away from them. Of every single moment that Makoto Naegi and Kyouko Kirigiri had been so clearly in love that they were the subject of all the class's gossip. Of when they were there for each other, as Hope's Peak seemed to crumble around them and they faced the threat that was among them.

The kiss was finally broken after what seemed like a blissful eternity, and Makoto fell back slightly in a daze. Kyouko stood, and gave her love a rare, bittersweet smile, knowing that that could be the last he saw of her.

[the rest of the story progresses as before, until]

Makoto Naegi awoke in the halls of Hope's Peak Academy. Typical. He had been knocked out more than anyone needs to be in their life, so regaining consciousness in a strange location was almost an everyday occurrence to him.

Getting up to collect himself, he instictively brushed any dust away from the front of his hoodie, but was quickly met by Sayaka Maizono, who approached him as soon as she spotted him. Sayaka pulled him into a friendly hug, so happy to see her former classmate from junior high school again. She whispered a few words into his ear, then ran away again, motioning Makoto in her direction. Makoto, still a little stunned, chose to move forward.

Passing a few doors to classrooms which were seemingly uninhabited, he spotted the Ultimate Baseball Star, Leon Kuwata, leaning with his back to the wall. From his position, Leon looked at Makoto and winked, giving him two thumbs up. A few doors later, he passed Chihiro Fujisaki, wearing that inimitable smile of his which seemed to brighten up the area around him. Turning a corner, he spotted Kiyotaka Ishimaru and Mondo Oowada arm in arm, the two bringers of order and disorder laughing heartily, linked like brothers. The next stretch of hallway saw him find Hifumi Yamada, who looked up from whatever 2D fantasy he was in to look at Makoto in understanding, as well as Celestia Ludenberg, who stared at him for a while before giving a rare, genuine smile. The next corner brought Makoto to the colossal frame of Sakura Oogami, who looked into his eyes as if proud of him for something he did not understand.

Following the hallway, in which the turns only seemed to become more frequent, he met Yasuhiro Hagakure, who stepped up to shake his hand and let out a slight chuckle afterwards. He was soon followed by Byakuya Togami, whose constant look of superiority was betrayed by a sense of thankfulness for everything Makoto had done. Of course, Touko Fukawa was alongside him, almost clinging to him, and she seemed to concur with the thoughts of her "Master" as always.

Finally after a myriad of turns, he had caught up to Sayaka, and she took him by the wrist, leading him to the doors of the gym hall. Flanking the doors were the "Sisters of Despair", Junko Enoshima and Mukuro Ikusaba. They had been his adversary in the past, but the two seemed completely different to what Makoto had remembered. Mukuro - a face Makoto was seeing once again for the first time - was shyer and quieter than the stone-faced killer her title would have suggested, looking into Makoto's eyes with something of a longing. Meanwhile, Junko seemed to have a much more genuine posture and a look of friendliness - perhaps even hope - in her eyes.

The sisters opened the doors, leading to a blinding light, while Sayaka ushered Makoto in.

The students and staff of Hope's Peak Academy all surrounded the gym hall, looking at him in true pride. He saw walls of faces he would never have expected to see again. And in the centre of the gym, Makoto was able to see the fallen body of the woman he loved. He stepped up to Kyouko, and squatted down to her level, taking her hand in his. Kyouko's eyes fluttered and opened, locking onto the kind, soft features of Makoto; just then, the corners of her mouth drew up into a smile. Makoto helped Kyouko up to her feet, holding her to allow her to stabilise herself. They looked into each other's eyes, and then threw their arms around each other in a tight embrace, as if the other would slip away again any moment. At that point, all around them began to applaud, watching the two lovers reunited once more, and thanking them for everything they had done. Junko and Sayaka were among the loudest cheerleaders, their very different voices heard over the wall of applause.

Kyouko, in the midst of all this, whispered into Makoto's ear: "If it had to happen like this... I'm glad we're together and safe again."

They kissed and held each other, not caring for anything around them, because they knew here, there would be no despair, no misfortune to get in their way. Hope was theirs once more.


End file.
